X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=5315d1a2802f91ea0d93ceae9a9e9140b12d031d;hb=9a729c9cc5344884e81a05b6f2d54c35d1104722;hp=2e4f4fecf21ead7e277c0ef0ee8ced96aa8d7ed9;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 2e4f4fe..5315d1a 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -1,13 +1,13 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
@@ -17,9 +17,12 @@
  */
 package jalview.datamodel;
 
-import java.util.*;
+import jalview.analysis.AlignSeq;
+
+import java.util.Enumeration;
+import java.util.Vector;
 
-import jalview.analysis.*;
+import fr.orsay.lri.varna.models.rna.RNA;
 
 /**
  * 
@@ -47,6 +50,8 @@ public class Sequence implements SequenceI
   String vamsasId;
 
   DBRefEntry[] dbrefs;
+  
+  RNA rna;
 
   /**
    * This annotation is displayed below the alignment but the positions are tied
@@ -54,7 +59,12 @@ public class Sequence implements SequenceI
    */
   Vector annotation;
 
-  /** array of seuqence features - may not be null for a valid sequence object */
+  /**
+   * The index of the sequence in a MSA
+   */
+  int index = -1;
+
+  /** array of sequence features - may not be null for a valid sequence object */
   public SequenceFeature[] sequenceFeatures;
 
   /**
@@ -116,7 +126,8 @@ public class Sequence implements SequenceI
 
   void checkValidRange()
   {
-    if (end < 1)
+    // Note: JAL-774 :
+    // http://issues.jalview.org/browse/JAL-774?focusedCommentId=11239&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#comment-11239
     {
       int endRes = 0;
       for (int j = 0; j < sequence.length; j++)
@@ -131,7 +142,10 @@ public class Sequence implements SequenceI
         endRes += start - 1;
       }
 
-      this.end = endRes;
+      if (end < endRes)
+      {
+        end = endRes;
+      }
     }
 
   }
@@ -569,20 +583,17 @@ public class Sequence implements SequenceI
     return this.description;
   }
 
-  /**
-   * Return the alignment position for a sequence position
-   * 
-   * @param pos
-   *          lying from start to end
+  /*
+   * (non-Javadoc)
    * 
-   * @return aligned position of residue pos
+   * @see jalview.datamodel.SequenceI#findIndex(int)
    */
   public int findIndex(int pos)
   {
     // returns the alignment position for a residue
     int j = start;
     int i = 0;
-
+    // Rely on end being at least as long as the length of the sequence.
     while ((i < sequence.length) && (j <= end) && (j <= pos))
     {
       if (!jalview.util.Comparison.isGap(sequence[i]))
@@ -893,8 +904,10 @@ public class Sequence implements SequenceI
     {
       this.annotation = new Vector();
     }
-
-    this.annotation.addElement(annotation);
+    if (!this.annotation.contains(annotation))
+    {
+      this.annotation.addElement(annotation);
+    }
     annotation.setSequenceRef(this);
   }
 
@@ -1170,4 +1183,30 @@ public class Sequence implements SequenceI
     }
   }
 
+  /**
+   * @return The index (zero-based) on this sequence in the MSA. It returns
+   *         {@code -1} if this information is not available.
+   */
+  public int getIndex()
+  {
+    return index;
+  }
+
+  /**
+   * Defines the position of this sequence in the MSA. Use the value {@code -1}
+   * if this information is undefined.
+   * 
+   * @param The
+   *          position for this sequence. This value is zero-based (zero for
+   *          this first sequence)
+   */
+  public void setIndex(int value)
+  {
+    index = value;
+  }
+  
+  public void setRNA(RNA r){rna=r;}
+  
+  public RNA getRNA() { return rna; }
+  
 }